> ## Documentation Index
> Fetch the complete documentation index at: https://wiki.latch.bio/llms.txt
> Use this file to discover all available pages before exploring further.

# Tools

> Internal capabilities and tools available to Latch Agent.

<Columns>
  <div>
    Latch Agent operates within [Latch Plots](/plots/overview) and has direct tools to manipulate the notebook environment. It can add, delete, and modify cells; execute code; and create interactive widgets for user interaction, and more.
  </div>

  <Frame>
    <img src="https://mintcdn.com/latchbio/O9ccDM5r9gHXixUG/images/agent/tools.png?fit=max&auto=format&n=O9ccDM5r9gHXixUG&q=85&s=d5f33c36c06b797958e3f0fd81106f12" alt="Tools" width="1920" height="980" data-path="images/agent/tools.png" />
  </Frame>
</Columns>

## Latch Plots Manipulation

Tools used to interact with and manipulate the Latch Plots notebook interface.

<AccordionGroup>
  <Accordion title="Cell Management" icon="square-plus">
    Manipulate notebook cells programmatically:

    * Create code cell
    * Create markdown cell
    * Edit cell
    * Delete cell
    * Delete all cells
    * Run cell
    * Stop cell

    Cells are automatically executed after creation or editing.
  </Accordion>

  <Accordion title="Notebook Organization" icon="file-text">
    Manage notebook structure and organization:

    * Rename notebook
    * Create tab
    * Rename tab
  </Accordion>

  <Accordion title="Restore Checkpoint" icon="clock-rotate-left">
    Revert the notebook to a previously-created checkpoint state.

    Useful when you are unhappy with recent prompt and notebook changes and want to revert the notebook state to the prompt before.
  </Accordion>

  <Accordion title="Interactive Widgets" icon="sliders">
    Generate and interact with widgets using the [Latch Plots library](/plots/widgets):

    * **Set widget value**: By widget key
    * **Auto-run code cells**: Configure widgets to automatically run code cells when values change

    Users can interact with widgets directly, triggering real-time updates.
  </Accordion>

  <Accordion title="H5AD Viewer Interaction" icon="eye">
    Interact with the H5AD viewer, a performant viewer widget in Latch Plots for single-cell and spatial data:

    **Data Visualization:**

    * **Change embeddings**: Switch between different embeddings (PCA, UMAP, t-SNE, etc.)
    * **Color by**: Set the viewer to color cells by a specific observation or variable
    * **Filter by range**: Set filters for an h5/AnnData widget to focus on specific data ranges
    * **Change marker opacity**: Adjust the opacity of cell markers in the visualization

    **View Controls:**

    * **Autoscale**: Reset the plotted view to Plotly's autoscaled data bounds
    * **Zoom**: Zoom the Plotly view in or out

    **Background Images:**

    * **Set background image**: Set a background image from user-attached file
    * **Toggle background visibility**: Show or hide a specific background image
    * **Open image aligner**: Open the image alignment modal

    **Data Management:**

    * **Manage observations**: Create or delete an observation column
    * **Add selected cells to category**: Assign selected cells to a categorical observation
  </Accordion>

  <Accordion title="Image Capture" icon="camera">
    Capture images of what's displayed in the notebook to help with analysis and decision-making:

    * **Capture widget image**: Take screenshots of h5/AnnData or plot widgets (Plotly, Matplotlib, Seaborn, etc.) displayed in the notebook
    * **Returns metadata**: Includes base64-encoded PNG images with visualization state (color\_by settings, filters, cell counts for h5 widgets)

    Use this to visually inspect plots, clustering results, or any Plotly-based visualization.
  </Accordion>

  <Accordion title="UI Guidance" icon="hand-pointer">
    Guide user attention and interaction:

    * **Spotlight UI element**: Highlight a UI element to draw attention to specific parts of the interface
  </Accordion>

  <Accordion title="Plan Management" icon="list-check">
    Manage the agent's analysis plan:

    * **Update plan**: Modify the structured plan during execution
    * **Submit response**: Final responses with status, questions, and summaries
  </Accordion>
</AccordionGroup>

## System Access

Tools used to interact with the underlying compute environment that powers Latch Plots.

<AccordionGroup>
  <Accordion title="Environment Management" icon="server">
    Manage the computational environment:

    * **Installing dependencies**: Install Python/R packages and system dependencies on demand
  </Accordion>

  <Accordion title="File System Operations" icon="folder">
    Interact with the local file system:

    * **Read file**: Optional offset and limit for large files (returns numbered lines)
    * **Search files**: Find files matching glob patterns (e.g., 'technology\_docs/\*.md')
    * **Search text**: Search for patterns using grep with line numbers (supports regex)
    * **Edit file**: Replace strings using search and replace operations
  </Accordion>

  <Accordion title="Code Execution" icon="code">
    Execute code and inspect variables:

    * **Execute Python code**: Run code in the notebook kernel and return results, stdout, stderr, and exceptions
    * **Inspect variables**: Get detailed information about global variables (type, shape, columns, dtypes) - especially useful for DataFrames and AnnData objects
  </Accordion>

  <Accordion title="Shell Commands" icon="terminal">
    Execute system and bash commands when needed for advanced operations:
  </Accordion>
</AccordionGroup>

## Analysis Capabilities

Latch Agent's analysis capabilities are based on partnerships with solution providers. We work with kit, assay, and instrument providers to build customized agents for each technology, ensuring best-in-class tools for each data type.

<AccordionGroup>
  <Accordion title="Redeem Packages" icon="gift">
    Redeem packages so the workspace gains access to technology-specific assets like data, workflows, and more.
  </Accordion>

  <Accordion title="Workflow Execution" icon="play">
    Launch registered Latch workflows, configure parameters, retrieve results, and monitor execution progress. The available workflows are based on our solution provider partnerships.

    #### Technology-Specific Workflows

    | Workflow                              | Technology                 | Utility                                                                                                                                          |
    | ------------------------------------- | -------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------ |
    | `xenium_preprocess_workflow`          | 10X Xenium                 | Preprocesses raw Xenium output into an analysis-ready .h5ad file. Run when user provides raw Xenium data without an existing H5AD.               |
    | `xenium_cell_segmentation_workflow`   | 10X Xenium                 | Re-segments cells using custom parameters or alternative segmentation methods when default Xenium segmentation is insufficient.                  |
    | `vizgen_cell_segmentation_wf`         | Vizgen MERFISH             | Performs cell segmentation on raw Vizgen MERSCOPE images. Required when starting from raw imaging data without pre-computed cell boundaries.     |
    | `domain_detection_wf`                 | 10X Xenium, Vizgen MERFISH | Identifies spatial domains/niches in tissue sections using clustering of spatial neighborhoods. Useful for discovering tissue microenvironments. |
    | `trekker_pipeline_wf`                 | Takara Trekker             | Processes raw FastQ files from Takara Trekker spatial experiments into analysis-ready outputs.                                                   |
    | `visium_spaceranger_to_h5ad_workflow` | 10X Visium                 | Converts Space Ranger output directories into .h5ad format for downstream analysis.                                                              |
    | `opt_workflow`                        | AtlasXOmics (DBiT-seq)     | Optimizes clustering parameters for spatial ATAC-seq data.                                                                                       |
    | `compare_workflow`                    | AtlasXOmics (DBiT-seq)     | Performs differential expression/accessibility analysis between groups or conditions.                                                            |

    #### Cross-Platform Workflows

    | Workflow                           | Technology                   | Utility                                                                                               |
    | ---------------------------------- | ---------------------------- | ----------------------------------------------------------------------------------------------------- |
    | `cell2location_workflow`           | Cross-platform (any spatial) | Performs cell type deconvolution using a single-cell reference. Maps cell types to spatial locations. |
    | `rapids_single-cell_preprocessing` | Cross-platform               | GPU-accelerated preprocessing for large single-cell/spatial datasets using RAPIDS.                    |
  </Accordion>

  <Accordion title="Domain Knowledge (Skills)" icon="book">
    Technology-specific analysis best practices are delivered through [skills](/agent/skills) — modular prompt packages that the agent loads on demand. Latch maintains a public set of skills covering platform APIs and technology workflows:

    * **Platform skills**: Widget APIs, data access patterns, and workflow launching for Latch Plots (`latch-plots-ui`, `latch-data-access`, `latch-workflows`, `latch-curation`)
    * **Technology skills**: Provider-specific analysis workflows, QC standards, and interpretation guidelines delivered as devkit skills (`takara-devkit`, `xenium-devkit`, `vizgen-devkit`, `atlasx-devkit`)

    Organizations can also register [custom skills](/agent/skills) from private GitHub repositories to add institutional conventions, internal workflows, or additional technology support.
  </Accordion>
</AccordionGroup>